This issue may possibly relate to differential treatment of fat saturation in the template vs the acquired images. We recommend fat-stat on for T1w images and off for T2w images.
Peace, Matt. From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Thursday, March 3, 2016 at 10:24 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Hi Matt, Thanks a lot, it worked. Those were the initial outputs for my first subject. I'm going to apply the pipeline to my whole data set soon; hope that such a problem never occurs. Thanks again for your taking time to sort this problem out, Xahra ________________________________ From: Glasser, Matthew [[email protected]<mailto:[email protected]>] Sent: Wednesday, March 02, 2016 1:30 AM To: Shams, Z. (Zahra); [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Is this a problem for only a single subject, or have you had issues with other subjects? If it is an isolated case, I might be inclined to recommend you: 1. Resample the T2w brain mask to T1w space using applywarp and ${StudyFolder}/${Subject}/T1w/xfms/T2w_reg_dc.nii.gz and nearest neighbor interpolation 2. Apply it to the unmasked images to generate properly brain masked data: ${StudyFolder}/${Subject}/T1w/T1w_acpc_dc.nii.gz ${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore.nii.gz ${StudyFolder}/${Subject}/T1w/T2w_acpc_dc.nii.gz ${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore.nii.gz 3. Rerun the module that does the final alignment to MNI space: ${GitRepo}/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=${StudyFolder}/${Subject}/MNINonLinear --t1=${StudyFolder}/${Subject}/T1w/T1w_acpc_dc \ --t1rest=${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore \ --t1restbrain=${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_brain \ --t2=${StudyFolder}/${Subject}/T1w/T2w_acpc_dc \ --t2rest=${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore \ --t2restbrain=${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore_brain \ --ref=${GitRepo}/global/templates/MNI152_T1_0.8mm.nii.gz \ --refbrain=${GitRepo}/global/templates/MNI152_T1_0.8mm_brain.nii.gz \ --refmask=${GitRepo}/global/templates/MNI152_T1_0.8mm_brain_mask.nii.gz \ --ref2mm=${GitRepo}/global/templates/MNI152_T1_2mm.nii.gz \ --ref2mmmask=${GitRepo}/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz \ --owarp=${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz \ --oinvwarp=${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz \ --ot1=${StudyFolder}/${Subject}/MNINonLinear/T1w \ --ot1rest=${StudyFolder}/${Subject}/MNINonLinear/T1w_restore \ --ot1restbrain=${StudyFolder}/${Subject}/MNINonLinear/T1w_restore_brain \ --ot2=${StudyFolder}/${Subject}/MNINonLinear/T2w \ --ot2rest=${StudyFolder}/${Subject}/MNINonLinear/T2w_restore \ --ot2restbrain=${StudyFolder}/${Subject}/MNINonLinear/T2w_restore_brain \ --fnirtconfig=${GitRepo}/global/config/T1_2_MNI152_2mm.cnf Matt. From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Tuesday, March 1, 2016 at 5:06 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Yes, it looks totally fine; the problem is just with T1w data. Xahra ________________________________ From: Glasser, Matthew [[email protected]<mailto:[email protected]>] Sent: Tuesday, March 01, 2016 11:13 PM To: Shams, Z. (Zahra); [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Out of curiosity, does the T2w brain extraction look better? Matt. From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Tuesday, March 1, 2016 at 3:31 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? I attached both MNI template and T1w_acpc nii.gz files with the image of overlaying one on the other. Thanks, Xahra ________________________________ From: Glasser, Matthew [[email protected]<mailto:[email protected]>] Sent: Tuesday, March 01, 2016 6:35 PM To: Shams, Z. (Zahra); [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? I need to be able to see the alignment with the template. Matt. From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Tuesday, March 1, 2016 at 2:54 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? T1 rigid alignment has been attached, but I can't see anything wrong with that. ________________________________ From: Glasser, Matthew [[email protected]<mailto:[email protected]>] Sent: Tuesday, March 01, 2016 12:25 AM To: Shams, Z. (Zahra); [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? What does the rigid alignment that precedes the brain extraction look like (i.e ${StudyFolder}/${Subject}/T1w/T1w_acpc.nii.gz Thanks, Matt. From: "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Monday, February 29, 2016 at 10:22 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Hi Matthew, Sorry for the long silence. I attached the raw T1w and T2w data as well as the one you asked for. and my call to PreFreeSurfer script is as follows: T1wInputImages=${StudyFolder}/${Subject}/T1w/T1w.nii.gz T2wInputImages=${StudyFolder}/${Subject}/T2w/T2w.nii.gz SpinEchoPhaseEncodePositive="NONE" DwellTime="NONE" SEUnwarpDir="NONE" TopupConfig="NONE" GEB0InputName="NONE" T1wSampleSpacing="0.0000092" #DICOM field (0019,1018) in s or "NONE" if not used T2wSampleSpacing="0.0000027" #DICOM field (0019,1018) in s or "NONE" if not used UnwarpDir="NONE" BrainSize="150" #BrainSize in mm, 150 for humans FNIRTConfig="${HCPPIPEDIR_Config}/T1_2_MNI152_2mm.cnf" GradientDistortionCoeffs="NONE" ## AtlasSpaceFolder="${StudyFolder}/${Subject}/MNINonLinear" ###### # template folders T1wTemplate="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm.nii.gz" T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain.nii.gz" T1wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz" T2wTemplate="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm.nii.gz" T2wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm_brain.nii.gz" T2wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T2_2mm.nii.gz" TemplateMask="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain_mask.nii.gz" Template2mmMask="${HCPPIPEDIR_Templates}/MNI152_T1_2mm_brain_mask_dil.nii.gz" sh ${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline_19022016.sh \ --path="$StudyFolder" \ --subject="$Subject" \ --t1="$T1wInputImages" \ --t2="$T2wInputImages" \ --t1template="$T1wTemplate" \ --t1templatebrain="$T1wTemplateBrain" \ --t1template2mm="$T1wTemplate2mm" \ --t2template="$T2wTemplate" \ --t2templatebrain="$T2wTemplateBrain" \ --t2template2mm="$T2wTemplate2mm" \ --templatemask="$TemplateMask" \ --template2mmmask="$Template2mmMask" \ --brainsize="$BrainSize" \ --fnirtconfig="$FNIRTConfig" \ --fmapmag="NONE" \ --fmapphase="NONE" \ --fmapgeneralelectric="NONE" \ --echodiff="NONE" \ --SEPhaseNeg="NONE" \ --SEPhasePos="NONE" \ --echospacing="$DwellTime" \ --seunwarpdir="$SEUnwarpDir" \ --t1samplespacing="$T1wSampleSpacing" \ --t2samplespacing="$T2wSampleSpacing" \ --unwarpdir="$UnwarpDir" \ --gdcoeffs="$GradientDistortionCoeffs" \ --avgrdcmethod="$AvgrdcSTRING" \ --topupconfig="$TopupConfig" \ --printcom=$PRINTCOM Thanks again, Xahra ________________________________ From: Glasser, Matthew [[email protected]<mailto:[email protected]>] Sent: Friday, February 26, 2016 8:17 PM To: Shams, Z. (Zahra); [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? We've not seen this particular issue before. Can you post some images of your raw data? Also, what does the registration look like for this file to the template: ${StudyFolder}/${Subject}/T1w/BrainExtraction_FNIRTbased/T1w_acpc_to_MNI_nonlin.nii.gz Also post your call to PreFreeSurfer. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Friday, February 26, 2016 at 4:21 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Hi Matthew, Thanks, I used the 0.8 template, but the problem still persists! I attached PreFreeSurfer T1 output to this post, I would appreciate any help or guide. Best regards, Xahra ________________________________ From: Glasser, Matthew [[email protected]<mailto:[email protected]>] Sent: Thursday, February 25, 2016 12:54 AM To: Shams, Z. (Zahra); [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Yes there are. Have a look at the ${GitRepo}/global/templates directory. See if using the 0.8mm templates helps. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Shams, Z. (Zahra)" <[email protected]<mailto:[email protected]>> Date: Wednesday, February 24, 2016 at 5:10 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] 0.8 template?Missing Some parts of the cortex in brain extraction? Dear all, I've just started working with HCP structural pipeline. I've got two questions! 1) In PreFreeSurfer step for processing my 0.8mm T1w and T2w images, I'm wondering if there are 0.8mm templates (in order to prevent upsampling my output to 0.7mm) I can use instead of those 0.7mm templates. 2) Output of the brain extraction step missed some small parts of the cortex, how can I improve the results? Many thanks for your time, Xara _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
